I have a file with a short probe each line (~10 letters in length, 1 million lines),and another chromosome file which can be viewed as a huge-size string (30 million letters). Now I want to find match position of each 'probe' against the 'chromosome' if matched. 
file1:
ATCGATGTGT
CCGATGCTGA
...

file2:
CCGATGCTGAggatgtcgcgcagatttaggCCGATGCTGAgagcatgaa...

[download]
Only one hit is possible for each 'probe' string. I read in the 2 files into variables: $chrom and @probes, respectively: 
  my $matched='';
        foreach (@probes){
                                chomp $_;
                                if ($chrom=~/$_/gi) {
                                my $position=pos($chrom);
                                $matched.= "$_\t$position\n";
                                }
         }

[download]
But using this method the script runs too slow for huge files. If there any quicker way around? Thanks. ^Appreciate your time!$

In reply to pattern match, speed problem by spring

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